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Aliases for ALKBH5 Gene

Aliases for ALKBH5 Gene

  • AlkB Homolog 5, RNA Demethylase 2 3 5
  • Oxoglutarate And Iron-Dependent Oxygenase Domain Containing 2 3
  • Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 5 3 4
  • Alkylated DNA Repair Protein AlkB Homolog 5 3 4
  • AlkB Family Member 5, RNA Demethylase 2 3
  • OFOXD1 3 4
  • ABH5 3 4
  • Probable Alpha-Ketoglutarate-Dependent Dioxygenase ABH5 3
  • AlkB, Alkylation Repair Homolog 5 (E. Coli) 2
  • AlkB, Alkylation Repair Homolog 5 3
  • RNA Demethylase ALKBH5 3
  • EC 1.14.11.- 4
  • OFOXD 3

External Ids for ALKBH5 Gene

Previous HGNC Symbols for ALKBH5 Gene

  • OFOXD1

Previous GeneCards Identifiers for ALKBH5 Gene

  • GC17P018031
  • GC17P018086
  • GC17P017840

Summaries for ALKBH5 Gene

GeneCards Summary for ALKBH5 Gene

ALKBH5 (AlkB Homolog 5, RNA Demethylase) is a Protein Coding gene. Diseases associated with ALKBH5 include Retinitis Pigmentosa 71 and Retinitis Pigmentosa 43. Among its related pathways are DNA Damage Reversal and DNA Double-Strand Break Repair. GO annotations related to this gene include poly(A) RNA binding and oxidative RNA demethylase activity.

UniProtKB/Swiss-Prot for ALKBH5 Gene

  • Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes (PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Can also demethylate N(6)-methyladenosine in single-stranded DNA (in vitro) (PubMed:24616105). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:21264265, PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Demethylation of m6A mRNA affects mRNA processing and export (PubMed:23177736). Required for spermatogenesis (By similarity).

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALKBH5 Gene

Genomics for ALKBH5 Gene

Regulatory Elements for ALKBH5 Gene

Enhancers for ALKBH5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G017356 1.3 Ensembl ENCODE dbSUPER 6.1 -826.8 -826778 0.6 CTCF RB1 ARID4B RAD21 GLIS2 PATZ1 ZNF143 SMC3 PRDM10 MIXL1 ALKBH5 GC17P017341 RPL13P12
GH17G017748 2 FANTOM5 Ensembl ENCODE dbSUPER 2.9 -429.2 -429243 10.3 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF143 ZNF286B USP32P2 ENSG00000264885 SMCR5 ENSG00000273018 LOC100419436 MPRIP-AS1 ENSG00000260647 TOM1L2 PEMT
GH17G017689 2 FANTOM5 Ensembl ENCODE dbSUPER 2.8 -487.7 -487688 12.1 HDGF PKNOX1 FOXA2 WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF286B ENSG00000264885 LOC100419436 UPF3AP1 SREBF1 FOXO3B FAM106A USP32P2 ENSG00000273018 DRG2
GH17G018157 0.9 ENCODE 0.3 -25.0 -25008 1.8 HDGF PKNOX1 ATF1 NFIB CREB3L1 EGR1 SCRT2 ZNF143 KLF7 RELB SHMT1 LOC105371568 ALKBH5
GH17G018163 0.6 ENCODE 0.4 -19.2 -19206 1.2 ZNF263 NR2F1 CEBPB CEBPG RELA ZNF592 MYNN NR2C1 NR2F6 SHMT1 MYO15A LOC105371568 ALKBH5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ALKBH5 on UCSC Golden Path with GeneCards custom track

Promoters for ALKBH5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000282660 1222 3401 CREB3L1 MLX ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263

Genomic Location for ALKBH5 Gene

Chromosome:
17
Start:
18,183,078 bp from pter
End:
18,209,954 bp from pter
Size:
26,877 bases
Orientation:
Plus strand

Genomic View for ALKBH5 Gene

Genes around ALKBH5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALKBH5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALKBH5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALKBH5 Gene

Proteins for ALKBH5 Gene

  • Protein details for ALKBH5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P6C2-ALKB5_HUMAN
    Recommended name:
    RNA demethylase ALKBH5
    Protein Accession:
    Q6P6C2
    Secondary Accessions:
    • B4DVJ4
    • D3DXC6
    • Q9NXD6

    Protein attributes for ALKBH5 Gene

    Size:
    394 amino acids
    Molecular mass:
    44256 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • Sequence=BAA91078.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ALKBH5 Gene

    Alternative splice isoforms for ALKBH5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ALKBH5 Gene

Post-translational modifications for ALKBH5 Gene

  • Ubiquitination at posLast=147147
  • Modification sites at PhosphoSitePlus

Other Protein References for ALKBH5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ALKBH5 Gene

Domains & Families for ALKBH5 Gene

Gene Families for ALKBH5 Gene

Protein Domains for ALKBH5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ALKBH5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6P6C2

UniProtKB/Swiss-Prot:

ALKB5_HUMAN :
  • Belongs to the alkB family.
Family:
  • Belongs to the alkB family.
genes like me logo Genes that share domains with ALKBH5: view

Function for ALKBH5 Gene

Molecular function for ALKBH5 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
N(6)-methyladenosine in mRNA + 2-oxoglutarate + O(2) = adenosine in mRNA + formaldehyde + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes (PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Can also demethylate N(6)-methyladenosine in single-stranded DNA (in vitro) (PubMed:24616105). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:21264265, PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Demethylation of m6A mRNA affects mRNA processing and export (PubMed:23177736). Required for spermatogenesis (By similarity).
UniProtKB/Swiss-Prot Induction:
By hypoxia, directly activated by HIF1A. Expression is regulated by PRMT7.

Enzyme Numbers (IUBMB) for ALKBH5 Gene

Gene Ontology (GO) - Molecular Function for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0016491 oxidoreductase activity IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IDA 21264265
GO:0035515 oxidative RNA demethylase activity TAS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ALKBH5: view
genes like me logo Genes that share phenotypes with ALKBH5: view

Animal Models for ALKBH5 Gene

MGI Knock Outs for ALKBH5:

Animal Model Products

CRISPR Products

miRNA for ALKBH5 Gene

miRTarBase miRNAs that target ALKBH5

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ALKBH5 Gene

Localization for ALKBH5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALKBH5 Gene

Nucleus speckle.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ALKBH5 gene
Compartment Confidence
nucleus 5
cytosol 5
golgi apparatus 5

Gene Ontology (GO) - Cellular Components for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 21264265
GO:0005654 nucleoplasm TAS --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IDA --
GO:0016607 nuclear speck IEA,IDA 23177736
genes like me logo Genes that share ontologies with ALKBH5: view

Pathways & Interactions for ALKBH5 Gene

genes like me logo Genes that share pathways with ALKBH5: view

Pathways by source for ALKBH5 Gene

Interacting Proteins for ALKBH5 Gene

Gene Ontology (GO) - Biological Process for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 21264265
GO:0006307 DNA dealkylation involved in DNA repair TAS --
GO:0006397 mRNA processing IMP 23177736
GO:0006406 mRNA export from nucleus IMP 23177736
GO:0007283 spermatogenesis ISS --
genes like me logo Genes that share ontologies with ALKBH5: view

No data available for SIGNOR curated interactions for ALKBH5 Gene

Drugs & Compounds for ALKBH5 Gene

No Compound Related Data Available

Transcripts for ALKBH5 Gene

mRNA/cDNA for ALKBH5 Gene

Unigene Clusters for ALKBH5 Gene

AlkB, alkylation repair homolog 5 (E. coli):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALKBH5 Gene

No ASD Table

Relevant External Links for ALKBH5 Gene

GeneLoc Exon Structure for
ALKBH5
ECgene alternative splicing isoforms for
ALKBH5

Expression for ALKBH5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ALKBH5 Gene

Protein differential expression in normal tissues from HIPED for ALKBH5 Gene

This gene is overexpressed in Breast (10.6), Peripheral blood mononuclear cells (7.4), Stomach (7.0), and CD8 Tcells (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ALKBH5 Gene



Protein tissue co-expression partners for ALKBH5 Gene

NURSA nuclear receptor signaling pathways regulating expression of ALKBH5 Gene:

ALKBH5

SOURCE GeneReport for Unigene cluster for ALKBH5 Gene:

Hs.744130

mRNA Expression by UniProt/SwissProt for ALKBH5 Gene:

Q6P6C2-ALKB5_HUMAN
Tissue specificity: Widely expressed, with highest expression in lung, followed by testis, pancreas, spleen and ovary.

Evidence on tissue expression from TISSUES for ALKBH5 Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Spleen(4.3)
  • Muscle(2.4)
  • Heart(2)
genes like me logo Genes that share expression patterns with ALKBH5: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ALKBH5 Gene

Orthologs for ALKBH5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALKBH5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALKBH5 34 35
  • 99.83 (n)
dog
(Canis familiaris)
Mammalia ALKBH5 34 35
  • 94.84 (n)
cow
(Bos Taurus)
Mammalia ALKBH5 34 35
  • 92.39 (n)
oppossum
(Monodelphis domestica)
Mammalia ALKBH5 35
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Alkbh5 34 16 35
  • 91.46 (n)
rat
(Rattus norvegicus)
Mammalia Alkbh5 34
  • 91.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ALKBH5 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALKBH5 34 35
  • 78.08 (n)
lizard
(Anolis carolinensis)
Reptilia ALKBH5 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia alkbh5 34
  • 75.24 (n)
zebrafish
(Danio rerio)
Actinopterygii alkbh5 34 35
  • 71.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10218 35
  • 46 (a)
OneToOne
Species where no ortholog for ALKBH5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ALKBH5 Gene

ENSEMBL:
Gene Tree for ALKBH5 (if available)
TreeFam:
Gene Tree for ALKBH5 (if available)

Paralogs for ALKBH5 Gene

No data available for Paralogs for ALKBH5 Gene

Variants for ALKBH5 Gene

Sequence variations from dbSNP and Humsavar for ALKBH5 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000028473 -- 18,203,458(+) ACACG(A/G)TAGGT intron-variant
rs1000091629 -- 18,203,974(+) AGGGG(A/C)CTTCC intron-variant
rs1000126381 -- 18,209,657(+) CAAGA(A/G)CAGAG utr-variant-3-prime
rs1000168103 -- 18,192,695(+) ATTAA(C/T)AGGTA intron-variant
rs1000297008 -- 18,188,650(+) AGGGG(C/G)GTTGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ALKBH5 Gene

Variant ID Type Subtype PubMed ID
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv510702 CNV deletion 20534489

Variation tolerance for ALKBH5 Gene

Residual Variation Intolerance Score: 11.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.29; 6.52% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ALKBH5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALKBH5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALKBH5 Gene

Disorders for ALKBH5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ALKBH5 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 71
  • rp71
retinitis pigmentosa 43
  • rp43
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for ALKBH5

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ALKBH5
genes like me logo Genes that share disorders with ALKBH5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ALKBH5 Gene

Publications for ALKBH5 Gene

  1. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. (PMID: 24778178) Xu C. … Min J. (J. Biol. Chem. 2014) 2 3 4 64
  2. Structure of human RNA N?-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. (PMID: 24489119) Aik W. … McDonough M.A. (Nucleic Acids Res. 2014) 3 4 64
  3. Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. (PMID: 24616105) Feng C. … Chen Z. (J. Biol. Chem. 2014) 3 4 64
  4. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. (PMID: 23177736) Zheng G. … He C. (Mol. Cell 2013) 3 4 64
  5. Human AlkB homologue 5 is a nuclear 2-oxoglutarate dependent oxygenase and a direct target of hypoxia-inducible factor 1alpha (HIF- 1alpha). (PMID: 21264265) Thalhammer A. … Pollard P.J. (PLoS ONE 2011) 3 4 64

Products for ALKBH5 Gene

Sources for ALKBH5 Gene

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